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Some nervous residents spent a night away from their Happy Valley homes, as hot-spots contined to smoulder at the scene of a large scrub fire.

About 35 residents from Rarangi Way and Happy Valley Rd in Wellington's southern suburb of Happy Valley fled their homes early on Thursday morning, as the fire spread in the dead of night, coming within metres of about half a dozen homes.

Fire-fighters and two helicopters with monsoon buckets battled the blaze all day yesterday.

Firefighters were called in to put out a flare-up at 5am this morning.

Crews from the Rural Fire Service kept watch on the site overnight, amid concerns strong southerly winds may whip the flames up again.

Light rain was falling at the scene this morning.

Resident Wayne Bowden said he and his family decided to stay the night after being reassured they were safe by fire crews.

However at least three of his neighbours stayed away, he said.

‘‘Some were a bit nervous, and decided to stay with family or friends.’’

Chris Sadler, who had fled the fire with his partner and five children, decided to stay at home.

‘‘It was ok, but we felt a bit uncomfortable at first. We were still a bit traumatised.’’

A joint Fire Service and police investigation started this morning.

It was thought the fire began near Landfill Rd.

"Scrub fires [in the middle of the night] are very, very rarely self-ignited - they don't just happen spontaneously," Fire Service Wellington area manager Peter Dempsey said."That's why there will be the initial suspicion put on the blaze."

Chief Rural Fire Officer Jock Darragh said they would remain at the scene to dampen down hot spots.

''A fire like this will take days to put out. There will be smokers all over the place,'' he said

A flare-up was reported at 5am, and was tackled with help from the Fire Service.

The fire could cost taxpayers up to $100,000, he said.

"It looked like the world was coming to an end [when I arrived]. Massive 50-foot flames and smoke."

Resident Terri Shaw said it was a shock to be woken in the night to hear there was a fire. "It was horrible, really distressing. You could hear the crackling of the fire and see all the smoke and sparks."

Later in the morning she watched as helicopters with monsoon buckets doused a flare-up, 50 metres from her Rarangi Way house. "We really have been blessed. It could have been a lot worse." Ms Shaw praised the hard work of firefighters.

Most residents who left their homes went to Owhiro Bay School, where they were looked after and given breakfast by staff and Civil Defence volunteers.

About 7.15am they were told they could return to their homes - an announcement that was met with applause.

Resident Caroline Freer said it was very scary, and she thought she was going to lose her house. "Our neighbour rang us at 2am and told us the whole hill was on fire and we had to get out. Shortly after the police came to evacuate us."

Happy Valley Rd resident Michelle Carlile-Alkhouri said she was woken by a neighbour banging on the door, telling her to get out. "It was just a ring of fire, it was massive, and it looked like it was encroaching on the development. It was pretty scary."